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Chapter 19
Gene Mutation and
DNA Repair, and
Genetics: Analysis &
Robert J. Brooker
© 2021 McGraw Hill. All rights reserved. Authorized only for instructor use in the classroom.
No reproduction or further distribution permitted without the prior written consent of McGraw Hill.
Introduction 1
The term mutation refers to a heritable change in the genetic
Mutations provide allelic variation
• On the positive side, mutations are the foundation for
evolutionary change needed for a species to adapt to
changes in the environment
• On the negative side, new mutations are much more likely
to be harmful than beneficial to the individual and often are
the cause of diseases
© McGraw Hill
Introduction 2
Understanding the molecular nature of mutations is a deeply
compelling area of research
Since mutations can be quite harmful, organisms have
developed ways to repair damaged DNA
Another topic explored in this chapter is homologous
recombination, which involves exchange of identical or
similar DNA segments between homologous chromosomes;
enhances genetic diversity; involved in DNA repair
© McGraw Hill
19.1 Effects of Mutations on Gene Structure and
Mutations can be:
• Changes in chromosome structure
• Changes in chromosome number
• Changes in DNA of a single gene
• Discussed in this chapter
• Mutations can affect the molecular and phenotypic
expression of genes
© McGraw Hill
Gene Mutations 1
Gene mutations are molecular changes in the DNA
sequence of a gene
A point mutation is a change in a single base pair
• It can involve a base substitution
• A transition is a change of a pyrimidine (C, T) to another
pyrimidine or a purine (A, G) to another purine
• A transversion is a change of a pyrimidine to a purine or
vice versa
• Transitions are more common than transversions
© McGraw Hill
Gene Mutations 2
Mutations may also involve the addition or deletion of short
sequences of DNA
© McGraw Hill
Gene Mutations Can Alter the Coding Sequence Within a
Gene 1
Mutations in the coding sequence of a protein-encoding gene can
have various effects on the polypeptide
• Silent mutations (mutaciones silenciosas) are those base
substitutions that do not alter the amino acid sequence of the
• Due to the degeneracy of the genetic code
• Missense mutations (mutación con cambio de sentido) are those
base substitutions in which an amino acid change does occur
• Example: Sickle cell disease (Refer to Figure 19.1)
• Unlike sickle cell disease, a missense mutation may have no
detectable effect on protein function, and the mutation is said
to be neutral. This is more likely to occur if the new amino
acid has similar chemistry to the amino acid it replaced
© McGraw Hill
Figure 19.1
© McGraw Hill
(a-b): ©Science History Images/Alamy
Missense Mutation in Sickle Cell Disease
(anemia falciformes)
A comparison of the amino acid sequence between normal β
globin and sickle cell β globin:
© McGraw Hill
Gene Mutations Can Alter the Coding Sequence Within a
Gene 2
Mutations in the coding sequence of a protein-encoding gene
can have various effects on the polypeptide
• Nonsense mutations (mutación sin sentido) are those
base substitutions that change a normal codon to a stop
• Frameshift mutations (cambio del marco de lectura)
involve the addition or deletion of a number of
nucleotides that is not divisible by three
• This shifts the reading frame so that translation of the
mRNA results in a completely different amino acid
sequence downstream of the mutation
© McGraw Hill
Gene Mutations Can Alter the Coding Sequence Within a
Gene 3
Access the text alternative for slide images.
© McGraw Hill
Gene Mutations Outside of Coding Sequences 1
Gene mutations outside of coding sequences can affect gene
expression and phenotype
Mutations in the core promoter can change levels of gene
• Up promoter mutations increase transcription
• Down promoter mutations decrease transcription
© McGraw Hill
Gene Mutations Outside of Coding Sequences 2
TABLE 19.2
Possible Consequences of Gene Mutations Outside of a
Coding Sequence
Effect of Mutation
May increase or decrease the rate of
Regulatory element/operator site
May disrupt the ability of the gene to be
properly regulated
May alter the ability of mRNA to be
translated; may alter mRNA stability
Splice recognition sequence
May alter the ability of pre-mRNA to be
properly spliced
© McGraw Hill
Gene Mutations Are Given Names That Describe How
They Affect Genotype and Phenotype
In a natural population, the wild-type is the relatively
prevalent genotype. Genes with multiple alleles may have
two or more wild-types.
• A forward mutation changes the wild-type genotype into
some new variation
• A reverse mutation changes a mutant allele back to the
• It is also termed a reversion
© McGraw Hill
Mutations Based on Their Effects on Wild-Type
Phenotype 1
Mutations can also be described based on their effects on
the wild-type phenotype
They are often characterized by their differential ability to
• Deleterious mutations decrease the chances of survival
The most extreme are lethal mutations
• Beneficial mutations enhance the survival or reproductive
success of an organism
• The environment can affect whether a given mutation is
deleterious or beneficial
© McGraw Hill
Mutations Based on Their Effects on Wild-Type
Phenotype 2
Some mutations are conditional
• They affect the phenotype only under a defined set of
• An example is a temperature-sensitive mutation
© McGraw Hill
Suppressor Mutations
Suppressor mutations reverse the phenotypic effects of another
A second mutation will sometimes counteract the effects of a
first mutation
These second-site mutations are called suppressor mutations
or simply suppressors
different to reversion
Intragenic suppressors
• The second mutation is within the same gene as the first
• Typically, the first mutation causes an abnormality in protein
structure and second mutation restores normal protein
© McGraw Hill
Intragenic Suppressor Mutations 1
TABLE 19.3
Examples of Suppressor Mutations
Type: Intragenic
No Mutation
Transport can occur
© McGraw Hill
Intragenic Suppressor Mutations 2
First Mutation (x)
Transport inhibited
Second Mutation (x)
Transport can occur
A first mutation disrupts normal protein function, and a
suppressor mutation affecting the same protein restores
function. In this example, the first mutation inhibits transport
function, and the second mutation restores it.
© McGraw Hill
Intergenic Suppressors
• The second mutation is in a different gene from the first
• Examples:
• Redundant function
• Common pathway
• Multimeric proteins
• Transcription factors
© McGraw Hill
Intergenic Suppressor – Redundant Function
Redundant function
A first mutation inhibits the function of a protein, and a
second mutation alters a different protein to carry out that
function. In this example, the proteins function as enzymes.
Access the text alternative for slide images.
© McGraw Hill
Intergenic Suppressor – Common Pathway
Common pathway
Two or more different proteins may function as enzymes in a
common pathway. A mutation that causes a defect in one
enzyme may be compensated for by a mutation that
increases the function of a different enzyme in the same
Access the text alternative for slide images.
© McGraw Hill
Intergenic Suppressor – Multimeric Protein
Multimeric protein
A mutation in a gene encoding one protein subunit that
inhibits function may be suppressed by a mutation in a gene
that encodes a different subunit. The double mutant has
restored function.
Access the text alternative for slide images.
© McGraw Hill
Intergenic Suppressor – Transcription Factor
Transcription factor
A first mutation causes loss of function of a particular protein.
A second mutation may alter a transcription factor and cause
it to activate the expression of another gene. This other gene
encodes a protein that can compensate for the loss of
function caused by the first mutation.
Access the text alternative for slide images.
© McGraw Hill
Changes in Chromosome Structure Can Affect Gene
A chromosomal rearrangement may affect a gene because
the chromosomal breakpoint (site of breaking and rejoining)
occurs within the gene
inversion or translocation
Alternatively, a gene may be left intact, but its expression
may be altered because of its new location
• This is termed a position effect
There are two common reasons for position effects:
1. Movement to a position next to regulatory sequences
2. Movement to a heterochromatic region
© McGraw Hill
Figure 19.2a
(a) Position effect due to regulatory sequences
Regulatory sequences are often bidirectional, so gene A may
now show the expression pattern of gene B
Access the text alternative for slide images.
© McGraw Hill
Figure 19.2b
(b) Position effects due to translocation to a
heterochromatic chromosome
Access the text alternative for slide images.
© McGraw Hill
Figure 19.3
(a) Normal eye
© McGraw Hill
(b) Variegated eye
(a-b): © Dr. Jack R. Girton
Mutations can Occur in Germ-Line or Somatic Cells
Geneticists classify animal cells into two types
• Germ-line cells
• Cells that give rise to gametes such as eggs and sperm
• Somatic cells
• All other cells
Germ-line mutations are those that occur directly in a
sperm or egg cell, or in one of their precursor cells
Somatic mutations are those that occur directly in a body
cell that is not part of the germ-line
© McGraw Hill
Effects of Germ-Line and Somatic Mutations
Germ-line mutations occur in gametes
• Passed to half of the gametes in the next generation; mutation
found in whole body
Somatic mutations result in patches of affected area
• The size of the patch will depend on the timing of the mutation.
The earlier the mutation, the larger the patch
• An individual with somatic regions that are genotypically
different from the rest of the body is called a genetic mosaic
• Mutations not present in gametes
© McGraw Hill
Figure 19.4
Access the text alternative for slide images.
© McGraw Hill
19.2 Random Nature of Mutations
Are mutations spontaneous occurrences or causally related
to environmental conditions?
This is a question that biologists have asked themselves for
a long time
Jean Baptiste Lamarck-physiological adaptation
• Proposed that physiological events (for example use and
disuse) determine whether traits are passed along to
Alternative possibility-random mutations
• Genetic variation occurs by chance
• Natural selection results in organisms with greater
reproductive success
© McGraw Hill
Experiment 19A: Testing the Random Mutation Theory 1
Joshua and Esther Lederberg studied the resistance of E.
coli to infection by bacteriophage T1
• tonr (T one resistance)
• They asked if tonr is due to spontaneous mutations that
occur at a low rate or to a physiological adaptation
• The physiological adaptation hypothesis predicts that the
number of tonr bacteria is very low unless there is selection
for T1 resistance
© McGraw Hill
Experiment 19A: Testing the Random Mutation Theory 2
• The random mutation hypothesis predicts that
mutations will happen randomly and will occur without
Hypothesis: Mutations are random events
© McGraw Hill
Experiment 19A Steps
1. Place individual bacterial cells onto growth media.
2. Incubate overnight to allow the formation of bacterial
colonies. This is called the master plate.
3. Press a velvet cloth (wrapped over a cylinder) onto the
master plate, and then lift gently to obtain a replica of
each bacterial colony. Press the replica onto 2 secondary
plates that contain T1 phage. Incubate overnight to allow
growth of mutant cells.
© McGraw Hill
Figure 19.6
Access the text alternative for slide images.
© McGraw Hill
Interpreting the Data
Resistant cells were in the same location on both plates.
• Mutations had occurred randomly in the absence of selection
by T1 (master plate)
• Became observable with selection but new colonies did not
appear due to the presence of T1
• Supports random mutation hypothesis, now called the random
mutation theory
© McGraw Hill
19.3 Spontaneous Mutations
Mutations can occur spontaneously or be induced
Spontaneous mutations
• Result from abnormalities in cellular/biological processes
• Errors in DNA replication, for example
• Underlying cause originates within the cell
Induced mutations
• Caused by environmental agents
• Agents that are known to alter DNA structure are termed
• These can be chemical (smoke) or physical agents (UV light)
Refer to Table 19.4 in your textbook
© McGraw Hill
Causes of Spontaneous Mutations
Spontaneous mutations can arise by three types of chemical
1. Depurination
2. Deamination
3. Tautomeric shift
© McGraw Hill
The removal of a purine (guanine or adenine) from the DNA forms
an apurinic site
The covalent bond between deoxyribose and a purine base is
somewhat unstable
• It occasionally undergoes a spontaneous reaction with water
that releases the base from the sugar
• Mammalian cells lose approximately 10,000 purines per 24
hours at 37°
Fortunately, apurinic sites can be repaired
• However, if the repair system fails, a mutation may result during
subsequent rounds of DNA replication
© McGraw Hill
Polymerase will add a random base
Figure 19.7
(a) Depurination
(b) Replication over an apurinic site
During replication, three out of four bases (A, T and G) are the
incorrect nucleotide
75% chance of a mutation
Access the text alternative for slide images.
© McGraw Hill
Deamination of Cytosine
Removal of an amino group from the cytosine base
• The other bases are not readily deaminated
DNA repair enzymes can recognize uracil as an
inappropriate base in DNA and remove it
• However, if the repair system fails, a C-G to A-T mutation
will result during subsequent rounds of DNA replication
© McGraw Hill
Figure 19.8a
(a) Deamination of cytosine
© McGraw Hill
Deamination of 5-methylcytosine
5-methylcytosine can be deaminated into thymine, a normal
constituent of DNA
Repair enzymes cannot determine which of the two bases on the
two DNA strands is the incorrect base
For this reason, methylated cytosine bases tend to create
hot spots for mutation
Fig. 19.8b
(b) Deamination of 5-methylcytosine
© McGraw Hill
Tautomeric Shift (tautómeros) tauto = igual y meros = parte)
A temporary change in base structure
The common, stable form of thymine and guanine is the keto
• Rarely, T and G convert to an enol form
The common, stable form of adenine and cytosine is the
amino form
• Rarely, A and C can convert to an imino form
© McGraw Hill
Figure 19.9a (1)
(a) Tautomeric shifts that occur in the 4 bases found in
© McGraw Hill
Figure 19.9a (2)
© McGraw Hill
Figure 19.9b
(b) Mistakes in base pairing
© McGraw Hill
Figure 19.9c
To cause mutation, a tautomeric shift must occur immediately
prior to replication
(c) Tautomeric shifts and DNA replication can cause
Access the text alternative for slide images.
© McGraw Hill
Oxidative Stress May Also Lead to DNA Damage and
Mutation 1
Aerobic organisms produce Reactive Oxygen Species
(ROS) including• Hydrogen peroxide
• Superoxide
• Hydroxyl radical
• Body tries to block buildup of ROS
• Enzymes such as superoxide dismutase and catalase
• Antioxidants
Oxidative stress: an imbalance between the production of
ROS and an organism’s ability to break them down
© McGraw Hill
Oxidative Stress May Also Lead to DNA Damage and
Mutation 2
ROS overaccumulation can lead to Oxidative DNA damage
For example, guanine can be converted to 7,8-dihydro-8oxoguanine (abbreviated 8-oxoG)
• Pairs with adenine during replication (transversion mutation)
• Causes GC base pair → TA base pair
Figure 19.10
© McGraw Hill
Mutations Due to Trinucleotide Repeats 1
Several human genetic diseases are caused by an unusual
form of mutation called trinucleotide repeat expansion
Certain regions of the chromosome contain trinucleotide
sequences repeated in tandem
• In individuals without disease symptoms, these sequences
are transmitted from parent to offspring without mutation
• However, in persons with TNRE disorders, the length of a
trinucleotide repeat has increased above a certain critical
• Disease symptoms occur
© McGraw Hill
Mutations Due to Trinucleotide Repeats 2
In some cases, the expansion is within the coding sequence
of the gene
Typically the trinucleotide expansion is CAG (glutamine)
Therefore, the encoded protein will contain long tracks of
• This causes the proteins to aggregate with each other
• This aggregation is correlated with the progression of the
disease, but may not cause disease symptoms
© McGraw Hill
Mutations Due to Trinucleotide Repeats 3
In other cases, the expansions are located in noncoding
regions of genes
• Some of these expansions are hypothesized to cause
abnormal changes in RNA structure
• Some produce methylated CpG islands which may
silence the gene
© McGraw Hill
Mutations Due to Trinucleotide Repeats 4
Some TNRE disorders progressively worsen in future
• May depend on which parent the mutant allele comes from
• In Huntington disease, the TNRE is more likely to occur
if inherited from the father
• In myotonic muscular dystrophy, the TNRE is more
likely to occur if inherited from the mother
• This suggests that TNRE can occur more frequently
during oogenesis or spermatogenesis, depending on
the gene involved
This is called anticipation
© McGraw Hill
Mechanism of Trinucleotide Repeat Expansion 1
TNREs contain at least one C and one G
• This allows formation of a hairpin
During DNA replication, a hairpin can lead to an increase or
decrease in the length of the DNA
• Polymerase can slip off DNA
• Hairpin forms and pulls strand back
• DNA polymerase hops back on
• Begins synthesis from new location
© McGraw Hill
Mechanism of Trinucleotide Repeat Expansion 2
These changes can occur during gamete formation
• Offspring will have very different numbers of repeats
Can also increase repeats in somatic cells
• This can increase severity of the disease with age
© McGraw Hill
Figure 19.11a
(a) Formation of a hairpin with a trinucleotide (CTG)
repeat sequence
© McGraw Hill
Figure 19.11b
(b) Mechanism of trinucleotide repeat expansion
Access the text alternative for slide images.
© McGraw Hill
19.4 Induced Mutations
Agents that alter the structure of DNA and thereby cause
mutations are called mutagens
The public is concerned about mutagens for two main
1. Mutagens are often involved in the development of human
2. Mutagens can cause gene mutations that may have harmful
effects in future generations
An enormous array of agents can act as mutagens
Mutagenic agents are usually classified as chemical or
physical mutagens
© McGraw Hill
Mutagens Alter DNA Structure in Different Ways
Chemical mutagens come in three main types:
1. Base modifiers
• Some covalently modify base structure
• Others disrupt pairing by alkylating bases
2. Intercalating agents
• Directly interfere with replication process
3. Base analogues
• Incorporate into DNA and disrupt structure
• Some tautomerize at a high rate
Physical mutagens include radiation:
• X-rays, gamma rays, ionizing radiation, UV light
© McGraw Hill
Base Modifiers
Base modifiers covalently modify the structure of a nucleotide
For example, nitrous acid replaces amino groups with keto groups
(–NH2 to =O)
This can change cytosine to uracil and adenine to hypoxanthine
• These modified bases do not pair with the appropriate
nucleotides in the daughter strand during DNA replication
Some chemical mutagens disrupt the appropriate pairing between
nucleotides by alkylating bases within the DNA
• Examples: Nitrogen mustards and ethyl methanesulfonate
© McGraw Hill
Figure 19.12
© McGraw Hill
Intercalating Agents
Intercalating agents contain flat planar structures that
intercalate themselves into the double helix
• This distorts the helical structure
• When DNA containing these mutagens is replicated, the
daughter strands may contain single-nucleotide additions
and/or deletions resulting in frameshifts
• Examples:
• Acridine dyes
• Proflavin
© McGraw Hill
Base Analogues
Base analogues become incorporated into daughter strands
during DNA replication
For example, 5-bromouracil is a thymine analogue
• It can be incorporated into DNA instead of thymine
• A tautomeric shift can result in pairing with guanine
© McGraw Hill
Figure 19.13a
(a) Base pairing of 5BU (a thymine analog) with adenine
or guanine
© McGraw Hill
Figure 19.13b
(b) How 5BU causes a mutation in a base pair during
DNA replication
Access the text alternative for slide images.
© McGraw Hill
Types of Physical Mutagens 1
Ionizing radiation
Includes X-rays and gamma rays
Has short wavelength and high energy
Can penetrate deeply into biological molecules
Creates chemically reactive molecules termed free radicals
Can cause
• Base deletions
• Oxidized bases
• Single nicks in DNA strands
• Cross-linking
• Chromosomal breaks
© McGraw Hill
Types of Physical Mutagens 2
Nonionizing radiation
• Includes UV light
• Has less energy
• Cannot penetrate deeply
into biological molecules
• Causes the formation of
cross-linked thymine
• Thymine dimers may
cause mutations when that
DNA strand is replicated
Fig. 19.14
© McGraw Hill
Mutation Rates and Frequencies 1
The term mutation rate is the likelihood that a gene will be
altered by a new mutation
• Commonly expressed as the number of new mutations in
a given gene per cell generation
• Range of 10-5 to 10-9 per generation
• Humans add 100-200 new mutations/generation
The mutation rate for a given gene is not constant
• It can be increased by the presence of mutagens
Mutation rates vary substantially between species and even
within different strains of the same species
© McGraw Hill
Mutation Rates and Frequencies 2
The mutation frequency for a gene is the number of mutant
genes divided by the total number of genes in a population
If 1 million bacteria were plated and 10 were mutant
• The mutation frequency would be 1 in 100,000 or 10-5
The mutation frequency is important in areas of genetics
such as population genetics
• Mutation frequencies may become greater than mutation
• Due to natural selection and genetic drift
© McGraw Hill
Testing Methods can Determine if an Agent is a Mutagen
Many different tests have been used to evaluate mutagenicity
One commonly used test is the Ames test
• Developed by Bruce Ames
• The test uses a strain of Salmonella typhimurium that cannot
synthesize the amino acid histidine
• It has a point mutation in a gene involved in histidine
• A second mutation (that is, a reversion) may occur, thereby
restoring the ability to synthesize histidine
• The Ames test monitors the rate at which this second mutation
© McGraw Hill
The Ames Test for Mutagenicity 1
Rat liver extract provides a mixture of enzymes that may
activate a mutagen
Different strains with transition, transversion or frameshift
mutations can be used
The control plate indicates that there is a low level of
spontaneous mutation
© McGraw Hill
The Ames Test for Mutagenicity 2
Mix together the
suspected mutagen, a
rat liver extract, and a
Salmonella strain that
cannot synthesize
histidine. The
suspected mutagen is
omitted from the
control sample.
Figure 19.15
Access the text alternative for slide images.
© McGraw Hill
19.5 DNA Repair
Because most mutations are deleterious, DNA repair
systems are vital to the survival of all organisms
• Living cells contain several DNA repair systems that can
fix different type of DNA alterations
• See Table 19.7 in your textbook
In most cases, DNA repair is a multi-step process
1. An irregularity in DNA structure is detected
2. The abnormal DNA is removed
3. Normal DNA is synthesized
© McGraw Hill
Damaged Bases Can Be Directly Repaired
In a few cases, the covalent modifications of nucleotides can be
reversed by specific enzymes
Photolyase can repair thymine dimers
• It splits the dimers restoring the DNA to its original condition
• Uses energy of visible light for photoreactivation
Alkyltransferase repairs alkylated bases
• It transfers the methyl or ethyl group from the base to a cysteine
side chain within the alkyltransferase protein
• Surprisingly, this permanently inactivates alkyltransferase
© McGraw Hill
Figure 19.16a
(a) Direct repair of a thymine dimer
© McGraw Hill
Figure 19.16b
(b) Direct repair of a methylated base
© McGraw Hill
Base Excision Repair Removes a Damaged Base
Base excision repair (BER) involves a category of enzymes
known as DNA N-glycosylases
• These enzymes can recognize an abnormal base and
cleave the bond between it and the sugar in the DNA
Depending on the species, this repair system can eliminate
abnormal bases such as
• Uracil; 3-methyladenine; 7-methylguanine
© McGraw Hill
Figure 19.17
Access the text alternative for slide images.
© McGraw Hill
Nucleotide Excision Repair Removes Damaged DNA
Segments 1
An important general process for DNA repair is nucleotide
excision repair (NER)
This type of system can repair many types of DNA damage,
• Thymine dimers and chemically modified bases
• Missing bases
• Some types of crosslinks
NER is found in all eukaryotes and prokaryotes
However, its molecular mechanism is better understood in
© McGraw Hill
Nucleotide Excision Repair Removes Damaged DNA
Segments 2
In E. coli, the NER system requires four key proteins
These are designated UvrA, UvrB, UvrC and UvrD
• Named as such because they are involved in Ultraviolet
light repair of pyrimidine dimers
• They are also important in repairing chemically damaged
UvrA, B, C, and D recognize and remove a short segment of
damaged DNA
DNA polymerase and ligase finish the repair job
© McGraw Hill
Figure 19.18
© McGraw Hill
Nucleotide Excision Repair Removes Damaged DNA
Segments 3
Several human diseases have been shown to involve
inherited defects in genes involved in NER
• These include xeroderma pigmentosum (XP), Cockayne
syndrome (CS) and PIBIDS
• A common characteristic of all three syndromes is an
increased sensitivity to sunlight
• XP can be caused by defects in seven different NER
© McGraw Hill
Figure 19.19
© McGraw Hill
© Anne Chadwick Williams/Sacramento Bee/ZUMAPRESS.com/Newscom
Mismatch Repair Systems Recognize and Correct a Base
Pair Mismatch 1
A base mismatch is another type of abnormality in DNA
The structure of the DNA double helix obeys the AT/GC rule
of base pairing
• However, during DNA replication an incorrect base may be
added to the growing strand by mistake
DNA polymerases have a 3’ to 5’ proofreading ability that
can detect base mismatches and fix them
If proofreading fails, the mismatch repair system comes to
the rescue
© McGraw Hill
Mismatch Repair Systems Recognize and Correct a Base
Pair Mismatch 2
Mismatch repair systems are found in all species
An important aspect of these systems is that they are specific
to the newly made strand
Molecular mechanism of mismatch repair in E. coli
• Three proteins, MutL, MutH and MutS detect the
mismatch and direct its removal from the newly made
• The proteins are named Mut because their absence leads to
a much higher mutation rate than normal
© McGraw Hill
Mismatch Repair Systems Recognize and Correct a Base
Pair Mismatch 3
A key characteristic of MutH is that it can distinguish between
the parental strand and the daughter strand
• Prior to replication, both parental strands are methylated
• Immediately after replication, the parental strand is
methylated whereas the newly made daughter strand is
© McGraw Hill
Mismatch Repair
The MutS protein slides
along the DNA and finds a
mismatch. The MutS/MutL
complex binds to MutH,
which is already bound to
a hemimethylated
Access the text alternative for slide images.
© McGraw Hill
Fig. 19.20
Double-Strand Breaks in DNA Can Be Repaired by
DNA double-strand breaks are very dangerous
• Breakage of chromosomes into pieces
• Caused by ionizing radiation and chemical mutagens
• Also caused by reactive oxygen species which are the
by-products of cellular metabolism
• 10 to 100 breaks occur each day in a typical human cell
• Breaks can cause chromosomal rearrangements and
• They may be repaired by two systems known as
homologous recombination repair (HRR) and
nonhomologous end joining (NHEJ)
© McGraw Hill
Repair of a Double-Strand Break by Homologous
Recombination 1
A double-strand break is processed by the short digestion of
the DNA strands
Sister chromatids are only available during S and G2 of cell
• Used for strand exchange
• Rarely, HRR can occur between non-identical chromosomes
© McGraw Hill
Repair of a Double-Strand Break by Homologous
Recombination 2
The unbroken strands are used as templates to synthesize
Strands are then broken and then rejoined in a way that
produces separate chromatids
• Because sister chromatids are genetically identical,
homologous recombination can be an error-free repair
© McGraw Hill
Figure 19.21 (1)
Access the text alternative for slide images.
© McGraw Hill
Figure 19.21 (2)
© McGraw Hill
Non-Homologous End Joining
Broken ends are recognized by end-binding proteins
• Formation of crossbridge
Processing may result in deletion of a small region
• Not error free
© McGraw Hill
Figure 19.22
Access the text alternative for slide images.
© McGraw Hill
Damaged DNA May Be Replicated by Translesion DNA
Polymerases 1
It is inevitable that some lesions may escape all repair
• Such lesions may be present when DNA is replicated
Replicative DNA polymerases, such as DNA pol III in E. coli,
are sensitive to geometric distortions in DNA
• They are unable to replicate through DNA lesions
• This type of replication requires specialized DNA
© McGraw Hill
Damaged DNA May Be Replicated by Translesion DNA
Polymerases 2
Specialized enzymes assist the replicative DNA polymerase
in the translesion synthesis (TLS) process
The translesion-replicating polymerases contain an active
site with a loose, flexible pocket
• They can accommodate aberrant structures in the
template strand
• A negative consequence of translesion-replicating
polymerases is their low fidelity
• The mutation rate is typically in the range of 10-2 to 10-3
• Much higher than 10-8 of replicative polymerase
© McGraw Hill
Damaged DNA May Be Replicated by Translesion DNA
Polymerases 3
When a replicative DNA polymerase encounters a damaged
region, it is swapped for a TLS polymerase
• Region is duplicated with error-prone replication
© McGraw Hill
19.6 Homologous Recombination
Homologous recombination involves crossing over
between identical or homologous regions of chromosomes
• It occurs in meiosis I and occasionally during mitosis
• Involves the alignment of a pair of homologous
chromosomes, followed by breakage at analogous
locations and exchange of corresponding segments
Crossing over that occurs between sister chromatids is called
sister chromatid exchange (SCE)
• Sister chromatids are genetically identical to each other
• SCE does not produce a new combination of alleles
Crossing over that occurs between homologous
chromosomes may produce new combinations of alleles
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Figure 19.23
(a) Sister chromatid exchange
(b) Recombination between homologous chromosomes
during meiosis
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The Holliday Model for Homologous Recombination
The Holliday model can account for the general properties of
homologous recombination during meiosis
Deduced from genetic crosses in fungi
A particularly convincing piece of evidence came from
electron micrographs of recombination structures
• The structure has been called a chi (χ) form
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Figure 19.24b
(b) Micrograph of a Holiday junction
From: H. Potter and D. Dressler, “DNA Recombination: In Vivo and In Vitro Studies,” Cold Spring Harb Symp
Quant Biol 1979.43: 969-985, © Cold Spring Harbor Laboratory Press. Image provided by Huntington Potter,
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Figure 19.24a (1)
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Figure 19.24a (2)
(a) The Holliday model for homologous recombination
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More Recent Models Have Refined the Steps of
More detailed studies of genetic recombination have led to a
refinement of the Holliday model
In particular, more recent models have modified the initiation
phase of recombination
• Two nicks in the same location on two strands is unlikely
• Rather, it is more likely for a DNA helix to incur a break in
both strands of one chromatid
• A double-strand break model was proposed by Jack
Szostak, Terry Orr-Weaver, Rodney Rothstein and
Franklin Stahl
• Requires DNA gap repair synthesis
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Figure 19.25 (1)
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Figure 19.25 (2)
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Various Proteins Facilitate Homologous Recombination 1
Molecular studies in two different yeast species suggest that
double-strand breaks initiate the homologous recombination
that occurs in meiosis
In other words, double-strand breaks create sites where a
crossover will occur
In Saccharomyces cerevisiae, formation of DNA doublestrand breaks requires at least 10 different proteins
• One of them, Spo11, is instrumental in actually breaking
the DNA
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Various Proteins Facilitate Homologous Recombination 2
Homologous recombination is found in all species
• The cells of any given species may have more than one
molecular mechanism for homologous recombination
The enzymology of homologous recombination is best
understood in E. coli
• Table 19.8 summarizes some of the proteins involved
• Note: The term Rec indicates that the proteins function in
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Table 19.8 E. coli Proteins that play a role in
Homologous Recombination
A complex of three proteins that tracks along the DNA and
recognizes double-strand breaks. The complex partially degrades
the double-stranded regions to generate single stranded regions
that can participate in strand invasion. RecBCD is also involved in
loading RecA onto single stranded DNA. In addition, RecBCD can
create single-strand breaks that are used to initiate homologous
Single-strand binding protein
Coats broken ends of chromosomes and prevents excessive
strand degradation.
Binds to single-stranded DNA and promotes strand invasion, which
enables homologous strands to find each other. It also promotes
the displacement of the complementary strand to generate a Dloop.
This protein complex binds to Holliday junctions. RuvAB promotes
branch migration. RuvC is an endonuclease that cuts the crossed
or uncrossed strands to resolve Holliday junctions into separate
RecG protein can also promote branch migration of Holliday
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Causes of Gene Conversion
Homologous recombination can cause two different alleles to
become identical alleles
• This process, whereby one of the alleles is converted to
the other, has been termed gene conversion
• The converted allele is close to the crossover site
Gene conversion can occur in one of two ways
1. DNA mismatch repair
• Refer to Figure 19.26
2. DNA gap repair synthesis
• Refer to Figure 19.27
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Figure 19.26
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Gap Repair Synthesis 1
Gene conversion by gap
repair synthesis according to
the double-strand break
The top chromosome carries
the recessive b allele, and the
bottom chromosome carries
the dominant B allele
Figure 19.27
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Gap Repair Synthesis 2
Both chromosomes carry the B allele.
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Figure 19.27
Study collections